Posted
by
timothyon Saturday September 06, 2008 @04:29PM
from the sounds-utterly-foolproof dept.

worromot writes "A group of geneticists published a method to determine if a given individual's DNA is present in a mixture (e.g., in a pool of blood on a carpet). An individual's DNA can comprise less than 1% of the mixture. (The article is in open access on PLoS Genetics website.) While this is a potential boon for forensics, there are more immediate worries about the privacy of the participants of the genetics studies that had been under way for many years. As Science magazine writes, 'The discovery that a type of genetic data that is widely shared and often posted online can be traced back to individuals has prompted the US National Institutes of Health and the Wellcome Trust to strip some genetic data from their publicly accessible Web sites and NIH to recommend that other institutions do the same.' The gravest worry was that an individual who had someone's genetic code could determine, based on the pooled data, whether the person participated in a disease study and whether they were in the disease group, or thereby glean private health information. NIH plans to ask institutions that have posted pooled data on their own Web sites to take these down, too."

Good luck with taking that stuff down. Posting something on the Internet is like spilling grape juice on a white cloth. If it wasn't made obvious by the age controversy over China's gymnasts, then I'll say it again: once something is on the Internet it stays there, no matter how much scrubbing you do. People need to think first and to not put something up if there is ever a chance it will be an issue.

It looks like you're essentially applying an evolutionary algorithm to mRNA expression data, which requires a run of many chips over a time series, over experimental parameters, and over sample replicates. These are genotype arrays. They cost less than a thousand bucks each and you only run one per individual (maybe several replicates). Plus the measurements are easier because it's a digital signal, so the scanners don't have to be terribly sophisticated. Already people are making ones as small as shoe boxes.

The "data mining" that would be involved would be the extraction of population data, but this has been done. And that was expensive, requiring lots of chips, but it only needs to be done once per population to derive a large amount of phenotypic information from a given genotype. And a lot of this data has already been published. For thousands of SNPs, we know which ones are associated with which phenotypes now, and with what probabilities. And Illumina just started selling a chip with 1.2 million SNP probes on it, if you're asking for a large enough scale.

Actually I wasn't referring to the expression time series work, that was interesting, but all it really demonstrated was that we aren't at the point of being able to do it in a useful fashion.

I was referring to the DNA pattern extraction, that requires a lot of work. I only applied it to promoters, but it has wider uses that are still being explored (including website similarity, oddly enough..). Pattern matching is required for data mining DNA, and we have only just started to get a grip on the very basics of the task.

On the whole my comment was based on the many hundreds of papers I've read on the subject, not my own work.

Do you have any idea how much DNA analysis costs?
About $350, the last time I checked. For about 500,000 genotypes per individual.

There is also a very major technology push for the "thousand-dollar genome", i.e. an ability to get a complete genome for $1000.

The core of the finding, by the way, is that the pooled data that everyone thought was completely safe for privacy point of view, is now no longer so. It is a problem for people who have agreed to take part in these studies (and that's a lot of people: a typical large scale study can involve 20,000 patients or more).

spent two years working on DNA analysis techniques... We, by which I mean the DNA analysis crowd
For what's it's worth, I've spent the last 15 years working on various DNA analysis techniques. I don't know about your "crowd", but the general genetics community takes issues of privacy quite seriously.

Honestly, there are big enough problems to solve without wasting time on sensationalist bullshit like this.

Bullshit yourself, idiot.

Technology, as they say, marches on. That's why someone who committed, or did not commit, a crime can be indicted or acquitted of the crime, even if it occurred twenty years before the DNA techniques were known. If this shit goes unchallenged now, ten years from now, the cops will be weeping on TV because they're being deprived of "this valuable crime-fighting tool". Jesus, everyone knows no LEO should ever be deprived of any "tool", no matter how ineffective it may be.

The worst goddanmed law my fellow Californians ever passed was the one a few years back when they voted to allow the pigs to seize a DNA sample from you at the time of arrest. No need to wait for arraignment or a trial. Of course, if you're not convicted, you can apply to have the sample destroyed. Idiots, APPLY means someone can turn down your APPLICATION. It should be a DEMAND, not a hat-in-hand APPLICATION, and there should be certifiable results. The same oversight standards should be applied to the destruction of the sample as were applied to the chain of evidence. As it stands, they can say they destroyed the sample and you'll never be allowed within a mile of any proof that they did so.

The "low copy count" method of multiplying a tiny sample of DNA to produce one large enough to make an identification has already been discredited in the UK (although the police continue to use it), and I can see this going the same way. A drop of blood will be found, the police will find some tiny sample of some poor guy who happened walk past that spot at some point and they will then have to fight it in court.

It's a shame the police can't be trusted to look at this and regulate their own use of it, but past experience with other DNA and fingerprint techniques has shown that they can't.